Archive for July, 2010

Poplar Growth Promoting Endophytic Bacterium

July 25th, 2010

enterobacterPoplar roots host a cortege of symbiotic endo- and ectomycorrhizal fungi. In addition to these well-known root-inhabiting microbes, the sequencing of the poplar genome has revealed the occurrence of hundreds of bacterial and fungal endophytes  in both roots and leaves. Some of these invasive bacteria actually help plants thrive. For example, the plant growth promoting endophytic bacterium Enterobacter sp. 638 can improve the growth of poplar on marginal soils by as much as 40%. The plant growth promoting gamma-proteobacterium was isolated from the stem of poplar (Populus trichocarpa x deltoides). Scientists at Brookhaven National Laboratory published the genome of Enterobacter on May 13, 2010 in PLoS Genetics. Their work identified a wide range of genes that help explain the symbiotic relationship between endophytic bacteria and plants. The genome sequence comprises a 4,5 Mbp chromosome and a 157 kbp plasmid. Analysis of the genome sequence, combined with metabolite analysis and quantitative PCR allowed the identification of an extended set of genes specific to the plant niche adaptation of Enterobacter. This includes genes that encode for proteins involved in survival in the rhizosphere (to cope with oxidative stress or uptake of nutrients released by plant roots), root adhesion, colonization/establishment inside the plant, plant protection against fungal and bacterial infections (siderophore production and synthesis of the antimicrobial compounds 4-hydroxybenzoate and 2-phenylethanol), and improved poplar growth and development through the production of the phytohormones indole acetic acid, acetoin, and 2,3-butanediol.

The molecular cross-talk between the partners requires a finely-tuned metabolic coordination and transcriptional regulation. The endophyte is responsible for the synthesis of a phytohormone, and a precursor for another, which poplar host is not able to produce, and the synthesis of the plant-growth promoting compounds requires in return the fate of plant-synthesized compounds, such as sucrose.

Together with inoculation of growth-promoting ectomycorrhizal fungi, such as Laccaria bicolor, Enterobacter and other endophytic bacteria can likely be exploited to improve establishment and sustainable production of poplar on marginal, non-agricultural soils.

Taghavi S, van der Lelie D, Hoffman A, Zhang Y-B, Walla MD, et al. (2010) Genome Sequence of the Plant Growth Promoting Endophytic Bacterium Enterobacter sp. 638. PLoS Genet 6(5): e1000943. doi:10.1371/journal.pgen.1000943.

Image Credit: Safiyh Taghavi and Dmytro Nykypanchuk (Brookhaven National Laboratory; image taken at the Center for Functional Nanomaterials)

Summer 2010 DOE JGI Newsletter

July 23rd, 2010

primerThe Summer 2010 edition of the DOE Joint Genome Institute newsletter, The Primer, has arrived and can be downloaded here: http//

Highlights include:

  • The Volvox genome Science publication
  • A report from the recent, “The Sequencing, Finishing, Analysis in the Future” Meeting
  • Amazonian Stinkbird guts (research/researcher) profile
  • California Biomass Collaborative’s Seventh Annual Forum report
  • Genomics educational flash cards (in exchange for your science highlights!)
  • and more!

Intermingling Ecosystems: An Alpine Valley

July 19th, 2010


Ribon Valley near Bessans (Haute-Maurienne, France)

Photo: © Francis Martin

Jupiter’s Beard Rust

July 19th, 2010

rusts_sempervivumAs you may know, my group is studying the poplar rust interaction and as a result, I got an eye for rust infections. Along the Ribon Valley trail near Bessans in Haute-Maurienne, I spotted several beautiful  hardy, succulent sempervivum (Sempervivum tectorum) (Jupiter’s Beard) in a meadow near the rim of the Rochemelon glacier. Many of them were infected by a rust fungus — likely Endophyllum sempervivi (Alb. & Schwein.) de Bary. Once in place, Endophyllum, a parasitic basidiomycete develops its mycelium inside the foliar tissues without producing necroses of these, and without showing any visible effect at first time. Nevertheless, more or less quickly, the infected leaf, arrived at adult state or nearly, continues or starts again to grow, and that in an immoderate manner. This excess growth doesn’t occur in every direction, but practically only in length. Thus, this infected leaf will reach quickly two, three or four times the normal size for the species, or even more … the rust fungus is clearly altering the leaf auxin metabolism. For additional details, see the Sempervivophilia site.

Photo: © Francis Martin

Parlez vous ‘Effectors’

July 19th, 2010

roc du mulinetBack Home after two weeks in the Alps and a visit to Oak Ridge National Lab in Tennessee. During my flight back to CDG, I finalized the draft of the editorial I wrote for the New Phytologist special issue dedicated to Effectors in Plant-Microbe Interactions (22nd New Phytologist Symposium, Versailles INRA Center, Paris, 13-16 September 2009). I outlined the draft when hiking along the alpine paths of the Vanoise National Park. The blooming meadows help me to find the inspiration. Here is the introduction:

[In the high valley of the Arc river in Haute Maurienne, glacier rivers and threatening seracs make loud roaring sounds, the snow is slowy retreating from the alpine meadows and hundred of plants are rushing to generate their seeds in these highlands were Winter lasts eight months.  In walking through this colorful cornocupia of flowering plants, enchanting forests of dwarf willows and rock lichens competing for light and nutrients – a peaceful struggle for life – it is hard to realize that a war is taking place in the entangled vegetal crowd.  Necrotic spots, blisters, yellow pustules are the visible testimony of the invasion of plant leaves and stem by bacterial and fungal deadly parasites …].

Photo: Roc du Mulinet – Glacier des Sources de l’Arc (Haute Maurienne, France) © F Martin